General technical questions

Where can I get help for a certain component/ option/ checkbox/ etc.?

Most elements in InCroMAP have tooltips. If you don't understand an option, you can get help in the first place by just pointing the mouse cursor over it and wait for the tooltip to show up (~ 3 seconds).

Is an internet connection required to run InCroMAP?

An internet connection is required for most operations. Many identifier mapping files and pathway-based visualizations require an active internet connection. However, if you import your data directly with NCBI Entrez Gene IDs and do not use the pathway-visualization or GO-enrichment, you should be able to run the application offline.

Where can I get the latest version?

Where can I get more information on the pathway translations?

I am behind a proxy server and keep getting the error "could not retrieve list of organism from KEGG".

Java provides its own means of configuring proxy servers for the JVM. Windows users may configure their proxy server as described here.
Users of all operating systems can specify proxy hosts as command-line options for the JVM as described by Oracle in this article.
If you require a proxy server for making connections to the internet, please start InCroMAP from the command-line with the following syntax:
java -Xms256m -Xmx1024m -Dhttp.proxyHost=MYPROXYHOST -Dhttp.proxyPort=MYPROXYPORT -Dftp.proxyHost=MYPROXYHOST -Dftp.proxyPort=MYPROXYPORT -DsocksProxyHost=MYPROXYHOST -DsocksProxyPort=MYPROXYPORT -jar InCroMAP.jar
Where -Xmx specifies the amount of memory available to the application and InCroMAP.jar needs to be replaced with the actual JAR file name of InCroMAP (e.g., InCroMAP1.3.0.jar).
Each occurrence of MYPROXYHOST should be replaced with the name of your proxy (e.g., webcache.mydomain.com) and each MYPROXYPORT must be replaced with the port number of your proxy (mostly 80 or 8080).
There are also parameters to specify the proxy username and password (-Dhttp.proxyUser and -Dhttp.proxyPassword). Please see several other resources for more information.

Starting the application / common errors and exceptions

Some operations need a lot of memory. If you simply start InCroMAP, without any JVM parameters, only 64 MB of memory are available. Please append the argument -Xmx1024M to start the application with 1 GB of main memory. See the documentation for a more detailed description of how to start the application with additional memory. If possible, you should give the application 2 GB of main memory. A minimum of 1 GB main memory should be available to the application.

Which Java version must be installed on my computer to launch InCroMAP?

Why does InCroMAP not start on my Mac with Mac OS prior to 10.6 Update 3?

If you try to launch InCroMAP, but the application does not start and you receive the
following error message on the command-line or Java console of your Mac, you need to
update your Java installation:
Exception in thread "AWT-EventQueue-0" java.lang.NoClassDefFoundError: com/apple/eawt/AboutHandler
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:703)
...
The interface com.apple.eawt.AboutHandler was introduced to Java for
Mac OS X 10.6 Update 3. If you have an earlier version of Mac OS or Java, please update your OS or
Java installation.
Also see the Mac OS documentation about the AboutHandler for more information.
On a Mac you can update your Java installation through the Software Update menu item in
the main Apple menu.

How can I change the look and feel of the application (colors and shapes)?

Please start InCroMAP with the JVM command-line parameter -Dswing.defaultlaf and specify your desired look and feel. For example,
java -Xms256m -Xmx1024m -Dswing.defaultlaf javax.swing.plaf.metal.MetalLookAndFeel -jar InCroMAP.jar
will start InCroMAP using Java's default look and feel. A list of other look and feels can be found here.

Content related questions / errors / exceptions

Which organisms are supported?

Currently mouse, human and rat are supported.

Can I import other microarray data types than the mentioned four?

Yes! Basically, everything that can be mapped to a gene can be imported. It is recommended to pick the mRNA data type (even if you don't have mRNA data), select any gene identifier and import your data as processed p-values or fold changes. With this method, you can perform integrated analysis, enrichment analysis and pathway-based visualization of basically every microarray type.

Is one node in a pathway always one gene?

No! KEGG often creates one node that groups multiple genes together. These can be either gene families (e.g. RRM1 and RRM2 in the pyrimidine metabolism) or functionally related genes. You should, in doubt, click on a node to see which genes are contained - this will also give you all expression values, associated to all genes that are contained in the node.

How can I save or export a picture/ table/ etc.?

You can save almost every table as tab-separated text file and every picture as JPEG or PNG file. Simply select "File" and "Save as" from the menu bar.

Error message while visualizing data in the pathway: no node matches the input data?

There are mainly two possible reasons for this error message. First, there really is no gene in the pathway contained in your source dataset. Second, it often occurs that people accidently mix organisms. If you show, for example, the "MAPK signaling pathway" for Homo sapiens and try to visualize a mouse dataset, you will also get this error. Please check on the pathway and on your source dataset that you picked the correct organism (it is shown for every tab at the bottom left corner of InCroMAP).

No targets could be annotated to my miRNA data?

This often occurs when you selected the wrong organism during import of your data. Please double-check that you selected the correct organism in the open-file dialog.

What does "Observation" or "Signal" mean?

The terms "Observation" or also "Signal" always refers to fold-changes or p-values. For example, if you have an experiment with some wild type mouse WT that has a spontaneous tumor and a somehow treated mouse TM that also has a tumor. Then, in this example the mRNA expression can be measured for WT healthy, WT tumor, MT healthy and MT tumor. You could now make several observations from this, e.g., "WT healthy vs. WT tumor" or "WT healthy vs. MT healthy", etc. Those observations are usually expressed as p-values or fold-changes and they are meant when talking of observations in InCroMAP.

Is it possible to import data directly from the GEO database?

Gene expression Omnibus (GEO) provides a tool called GEO2R. This can be used perfectly to export data from GEO into InCroMAP. You can call it either directly from the given URL or by clicking on the "Analyze with GEO2R" link that is shown at the bottom of each GEO series. After successfully using this tool (at the top of the GEO2R page is a link to a tutorial video) you can click the "Save all results" link and store the result somewhere on your computer. You maybe need to use the "save page as" function of your browser. Afterwards, please open this file in InCroMAP, assign observations to all p-values and fold changes (logFC) and use the gene symbols as identifiers.

Is it possible to fix missing links in pathways?

Missing side-reactants of metabolic pathways can be included by activating the "Autocomplete reactions" option in "Preferences", "KEGGtranslator options". Missing links in metabolic pathways can be fixed by including reaction nodes. Therefore, please open the preferences, select "KEGGtranslator options" and activate "Include nodes for metabolic reaction". However, activating these two options might reduce the clarity of some pathways by putting too many information in them.
Missing links in signaling pathways unfortunately cannot be restored. However, by underlying the original KEGG image in the background, they can be made visible to the user (ensure option "Show KEGG picture in graph background", which can be found in "Preferences", "Graph options" is selected).